Hymenobacter sedentarius sp. nov., isolated from a soil

J Microbiol. 2016 Apr;54(4):283-9. doi: 10.1007/s12275-016-5386-3. Epub 2016 Apr 1.

Abstract

A novel Gram-negative and red-pinkish bacterium designated DG5B(T) was isolated from a dry soil. Cells were rods that were catalase- and oxidase-positive, and non-motile. The strain was found to grow at temperatures from 10 to 30°C (optimum 25°C) and pH 6.0-8.0, (optimum pH 7) on R2A broth. 16S rRNA gene sequence (1,452 bp) analysis of this strain identified it as a member of the genus Hymenobacter that belongs to the class Cytophagia. The highest gene sequence similarities were with Hymenobacter arizonensis OR362-8(T) (98.3%), Hymenobacter humi DG31A(T) (97.6%), and Hymenobacter glaciei VUG-A130(T) (96.6%). Strain DG5B(T) exhibited <70% DNA-DNA relatedness with H. arizonensis (34.7 ± 7.0%; reciprocally, 29.7 ± 1.2%) and H. humi (39.4 ± 4.3%; reciprocally, 39.5 ± 3.3%) as a different genomic species, and its genomic DNA G+C content was 59.8%. Strain DG5B(T) had the following chemotaxonomic characteristics: the major fatty acids are iso-C15:0, anteiso-C15:0, C16:1 ω5c, and summed feature 3 (C16:1 ω7c / C16:1 ω6c); polar lipid profile contained phosphatidylethanolamine (PE), unknown aminophospholipid (APL), unknown glycolipids (GL), unknown phospholipids (PL), and unknown polar lipids (L); the major quinone is MK-7. The absorbance peak of pigment is at 481.0 nm. Strain DG5B(T) showed low-level resistance to gamma-ray irradiation. Phenotypic, chemotaxonomic, and genotypic properties indicated that isolate DG5B(T) represents a novel species within the genus Hymenobacter for which the name Hymenobacter sedentarius sp. nov. is proposed. The type strain is DG5B(T) (=KCTC 32524(T) =JCM 19636(T)).

Keywords: Hymenobacter; soil; taxonomy.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Bacteroidetes / classification*
  • Bacteroidetes / cytology
  • Bacteroidetes / isolation & purification*
  • Bacteroidetes / physiology
  • Base Composition
  • DNA, Bacterial / chemistry
  • DNA, Bacterial / genetics
  • Gamma Rays
  • Genes, rRNA
  • Hydrogen-Ion Concentration
  • Lipids / analysis
  • Nucleic Acid Hybridization
  • Phenotype
  • Phylogeny
  • RNA, Ribosomal, 16S / genetics
  • Seoul
  • Soil Microbiology*
  • Temperature

Substances

  • DNA, Bacterial
  • Lipids
  • RNA, Ribosomal, 16S